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#protein folding Open access Oct 2026

Recurrent catalytic-site change and electrostatic remodeling across the HEPN ribonuclease fold.

Together, these results establish recurrent catalytic-state change and physicochemical remodeling of the ancestral HEPN cleft, whether such remodeling corresponds to altered binding, regulation, or another molecular function remains a hypothesis requiring experimental testing.

M. Zimmer · 0 citations
Sep 2026

Ground-state chromophore geometry, not cage size, tracks quantum yield in fluorescent proteins.

A common explanation for brightness variation in fluorescent proteins (FPs) is that tight chromophore cages produce bright proteins. This model predicts that quantum yield should track the dihedral rotational space available to the chromophore. We tested that prediction across 838 FP crystal structures from the Protein...

M. Zimmer · 1 citation
Open access Aug 2026

Barrel Shape and Chromophore Rigidity Predict Fluorescent-Protein Photophysics

Cross-sectional barrel geometry across 908 FP crystal structures in the RCSB PDB is analyzed by principal component analysis (PCA)-based axis determination and convex hull analysis of protein-atom slices at the chromophore plane; 780 structures (210–245 residues, with the chromophore-containing chain selected in FP-com...

Luke P. Begg, Madeline L. Mason, M. Zimmer · 0 citations
Open access Aug 2026

Discovery of a buried charge-network GFP-fold family spanning prokaryotes and eukaryotes

Findings expand the known sequence and chemical space of the GFP barrel, although the biochemical function of the network remains unknown, and identify the same two-cation/two-anion/tyrosine network in 238 members of DUF2490, an unrelated outer-membrane beta-barrel family consistent with convergent evolution of the bur...

T. L. Schneider, M. Zimmer · 0 citations

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